Bioinformatics Command Line Hacks

Your Go-To Resource for Efficient Data Processing

Overview

This repository is a curated collection of powerful command-line snippets, scripts, and best practices tailored for bioinformatics tasks. Whether you're wrangling large datasets on an HPC cluster, automating repetitive steps, or just looking for a quicker way to get things done, you'll find useful hacks here.

The aim is to provide practical, copy-paste ready solutions that enhance productivity and streamline bioinformatics workflows.

Motivation

Bioinformatics often involves repetitive tasks and complex data manipulations from the command line. Many researchers find themselves writing the same small scripts or searching for common solutions. This repository aims to centralize these "hacks" to save time, reduce errors, and foster a collaborative environment for sharing knowledge.

How to Use

The repository is structured into distinct categories to help you quickly navigate and find the relevant hacks:

• SLURM-hacks/: Tips, templates, and scripts for managing jobs on SLURM-based High-Performance Computing (HPC) clusters, including array jobs.
• command-line-hacks/: General command-line utility tips, Bash scripting techniques, and common text/file manipulation tricks applicable across various domains.
• bioinformatics-hacks/: Specific command-line solutions and snippets for common bioinformatics file formats (FASTQ, BAM, VCF, FASTA, BED) and tasks.

Simply browse the directories, open the README.md files within them, and discover the snippets you need.

Contribution Guidelines

Contributions are highly encouraged! If you have a useful command-line hack, a SLURM script, or a bioinformatics snippet that you frequently use, please consider sharing it.

To contribute:

1. Fork this repository.
2. Create a new branch for your feature or fix (git checkout -b feature/your-hack).
3. Add your hack(s) to the appropriate directory.
   • Create a new Markdown file (.md) for more extensive explanations or multiple related hacks.
   • Add snippets directly to the directory's README.md for simpler, short tips.
   • Ensure all code snippets are well-commented and explained.
4. Update the relevant README.md file (within the subdirectory) to briefly describe your addition.
5. Commit your changes (git commit -m "Add description of your hack").
6. Push to your branch (git push origin feature/your-hack).
7. Create a Pull Request to the main branch of this repository.

Please ensure your contributions are well-documented, tested, and follow good command-line practices.